GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Magnetospirillum magneticum AMB-1

Align glucose transporter, ATPase component (characterized)
to candidate WP_011384921.1 AMB_RS12790 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF3641
         (260 letters)



>NCBI__GCF_000009985.1:WP_011384921.1
          Length = 232

 Score = 88.6 bits (218), Expect = 1e-22
 Identities = 71/231 (30%), Positives = 118/231 (51%), Gaps = 16/231 (6%)

Query: 11  GATPLVEMKDISISFGG----IKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQ 66
           G   L E+  I+  FG     + A+  V + L+PGEVVGLLG +G+GKSTL+ ++    +
Sbjct: 3   GPQVLAELTGIAKHFGEGASRVDALRGVDLSLHPGEVVGLLGPSGSGKSTLLNIIGCVVE 62

Query: 67  MDAGEIRVNGDKV-----EITNPRDARSHNIETIYQTLALADNLDAASNLFLGRELVTPF 121
            +AG + ++G  V        + R  R   I  I+Q   L   L++  N+ +  EL    
Sbjct: 63  PNAGRMVLDGVVVYDGAWTGGDLRRLRLDKIGFIFQFHNLLPFLNSRDNVAVVLELAGQ- 121

Query: 122 GLVDDSAMEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPT 181
              D +A      ++++ L    +  + P   LSGG+ Q VAIARA+  N ++++ DEPT
Sbjct: 122 ---DPAAARRRAGELLDYLEVGARAEASP-GQLSGGEAQRVAIARALANNPRLILADEPT 177

Query: 182 AALGPHETQMVAE-LIQQLKAQGIGIFLIDHDVNAVMELCDRASVMKNGQL 231
           AAL      +V + LI+  + Q   + ++ HD   + +  DR   +++G L
Sbjct: 178 AALDSQRAAIVMDLLIKVAREQNAAVLVVSHD-EKIYDRFDRMVRVRDGVL 227


Lambda     K      H
   0.317    0.135    0.373 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 141
Number of extensions: 8
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 260
Length of database: 232
Length adjustment: 24
Effective length of query: 236
Effective length of database: 208
Effective search space:    49088
Effective search space used:    49088
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory